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Journal Publications


Artificial sweeteners induce glucose intolerance by altering the gut microbiota.
Suez J, Korem Tal, Zeevi David, Zilberman-Schapira G, Thaiss CA, Maza O, Israeli D, Zmora N, Gilad S, Weinberger Adina, Kuperman Y, Harmelin A, Kolodkin-Gal I, Shapiro H, Halpern Z, Segal Eran, Elinav E.  
Nature 2014 Sep. doi: 10.1038/nature13793
 
In pursuit of design principles of regulatory sequences
Levo Michal, Segal Eran  
Nature Reviews Genetics 2014 Jun. 10;doi:10.1038/nrg3684
 
Landscape and variation of RNA secondary structure across the human transcriptome
Wan Y, Qu K, Zhang QC, Flynn RA, Manor Ohad, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal Eran, Chang HY.  
Nature 2014 Jan 30;505(7485):706-9. doi: 10.1038/nature12946  
See also: Nature Reviews Genetics Highlight
 
The grammar of transcriptional regulation
Weingarten-Gabbay Shira, Segal Eran  
Human Genetics 2014 Jan 5.;PMID:24390306
 
Fixated on fixation - using ChIP to interrogate the dynamics of chromatin interactions.
Leeat Keren and Eran Segal  
Genome Biology 2013 Nov 21;14(11):138
 
Promoters maintain their relative activity levels under different growth conditions
Leeat Keren, Ora Zackay, Maya Lotan-Pompan, Uri Barenholz, Erez Dekel, Vered Sasson, Guy Aidelberg, Anat Bren, Danny Zeevi, Adina Weinberger, Uri Alon, Ron Milo and Eran Segal  
Molecular Systems Biology 2013 Oct. 29;9:701
 
Predicting disease risk using bootstrap ranking and classification algorithms.
Ohad Manor and Eran Segal  
PLoS Comput. Biol. 2013 Aug;9(8):e1003200.;doi: 10.1371/journal.pcbi.1003200
 
Nucleosome maps of the human cytomegalovirus genome reveal a temporal switch in chromatin organization linked to a major IE protein.
Einat Zalckvara, Christina Paulus, Desiree Tilloa, Alexandra Asbach-Nitzschec, Yaniv Lubling, Carla Winterling, Nicholas Strieder, Katrin Mucke,Felicia Goodrum, Eran Segal and Michael Nevels  
Proc. Natl. Acad. Sci. 2013 Aug 6;110(32):13126-31. doi: 10.1073/pnas.1305548110
 
Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast.
Shlomi Dvir, Lars Velten, Eilon Sharon, Danny Zeevi, Lucas B. Careya, Adina Weinberger and Eran Segal  
Proc. Natl. Acad. Sci. 2013 Jul 23;110(30):E2792-801. doi: 10.1073/pnas.1222534110
 
Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise.
Maya Dadiani, David van Dijk, Barak Segal, Yair Field, Gil Ben-Artzi, Tali Raveh-Sadka, Michal Levo, Irene M. Kaplow, Adina Weinberger, Eran Segal.  
Genome Res., 2013 Jun;23(6):966-76  
See also: Genome Research Cover
 
Sequence features of yeast and human core promoters that are predictive of maximal promoter activity.
Shai Lubliner, Leeat Keren, Eran Segal  
Nucleic Acids Res. 2013 Jun 1;41(11):5569-81.
 
Promoter sequence determines the relationship between expression level and noise
Lucas B Carey , David van Dijk, Sloot PM, Kaandorp JA, Eran Segal  
PLoS Biol. 2013 Apr;11(4):e1001528
 
Robust prediction of expression differences among human individuals using only genotype information.  
Ohad Manor, Eran Segal  
PLoS Genet. 2013 Mar;9(3):e1003396
 
Measurements of the impact of 3' end sequences on gene expression reveal wide range and sequence dependent effects
Ophir Shalem, Lucas Carey, Danny Zeevi, Eilon Sharon, Leeat Keren, Adina Weinberger, Orna Dahan, Yitzhak Pilpel and Eran Segal  
PLoS Comput Biol. 2013 Mar;9(3):e1002934
 
Determinants of nucleosome positioning.
Kevin Struhl and Eran Segal  
Nat. Struct Mol Biol., 2013 Mar;20(3):267-73.
 
Genomics: ENCODE explained
Joseph R. Ecker, Wendy A. Bickmore, Ines Barroso, Jonathan K. Pritchard, Yoav Gilad and Eran Segal  
Nature, 2012 Sep 6;489(7414):52-5.
 
Genome-wide Measurement of RNA Folding Energies
Yue Wan, Kun Qu, Zhengqing Ouyang, Michael Kertesz, Jun Li, Robert Tibshirani, Debora L. Makino, Robert C. Nutter, Eran Segal, Howard Y. Chang  
Molecular Cell, Sep 2012, doi:10.1016/j.molcel.2012.08.008  
See also: Faculty of 1000 review
 
Cell lineage analysis of the mammalian female germline
Yitzhak Reizel, Shalev Itzkovitz, Rivka Adar, Judith Elbaz, Adrian Jinich, Noa Chapal-Ilani, Yosef E. Maruvka, Nava Nevo, Zipora Marx, Inna Horovitz, Adam Wasserstrom, Avi Mayo, Irena Shur, Dafna Benayahu, Karl Skorecki, Eran Segal, Nava Dekel and Ehud Shapiro  
PLoS Genetic, February 2012 ,doi:10.1371/journal.pgen.1002477
 
New insights into replication origin characteristics in metazoans
Christelle Cayrou, Philippe Coulombe, Aurore Puy, Stephanie Rialle, Noam Kaplan, Eran Segal and Marcel Mechali  
Cell Cycle, 2012 Feb;11(4):658-67.
 
Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
Tali Raveh-Sadka, Michal Levo, Uri Shabi, Boaz Shany, Leeat Keren, Maya Lotan-Pompan, Danny Zeevi, Eilon Sharon, Adina Weinberger & Eran Segal  
Nature Genetics, May 2012, doi:10.1038/ng.2305  
See also: Faculty of 1000 review, News and Views in Nature Generics
 
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
Eilon Sharon, Yael Kalma, Ayala Sharp, Tali Raveh-Sadka, Michal Levo, Danny Zeevi, Leeat Keren, Zohar Yakhini, Adina Weinberger & Eran Segal  
Nature Biotechnology, May 2012, doi:10.1038/nbt.2205  
See also: Highlight in Nature Biotechnology News and Views
 
Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters.
Zeevi D, Sharon E, Lotan-Pompan M, Lubling Y, Shipony Z, Raveh-Sadka T, Keren L, Levo M, Weinberger A, Segal E  
Genome Res., 2011 Dec;21(12):2114-28
 
Understanding the transcriptome through RNA structure.
Yue Wan, Michael Kertesz, Robert Spitale, Eran Segal, Howard Chang  
Nature Reviews Genetics 2011, 12(9):641-55
 
Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes.
Michal Rabani, Michael Kertesz, Eran Segal  
Methods Mol Biol. 2011;714:467-79.
 
How transcription factors identify regulatory sites in genomic sequence.
Yari Field, Eilon Sharon, Eran Segal  
Subcell Biochem. 2011;52:193-204.
 
High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans.
Sevinc Ercan, Yaniv Lubling, Eran Segal, Jason D Lieb  
Genome Res., 2011 Feb;21(2):237-44
 
Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast.
Ephraim Kenigsberg, Amir Bar, Eran Segal, Amos Tanay  
PLoS Comput Biol. 2010 Dec 23;6(12):e1001039.PMID: 21203484
 
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.
Gerstein MB et al.  
Science 2010, 24 December 2010:24 December 2010:DOI: 10.1126/science.1196914
 
Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology
Noam Kaplan, Timothy R Hughes, Jason D Lieb, Jonathan Widom, Eran Segal  
Genome Biology 2010, 11:140 doi:10.1186/gb-2010-11-11-140
 
Overlapping codes within protein-coding sequences
Shalev Itzkovitz, Eran Hodis, Eran Segal  
Genome Res. 2010 Sep 14. [Epub ahead of print]
 
Genome-wide measurement of RNA secondary structure in yeast
Michael Kertesz, Yue Wan, Elad Mazor, John L.Rinn, Robert C.Nutter, Howard Y.Chang, Eran Segal  
Nature Nature 467, 103-107 (02 September 2010) | doi:10.1038/nature09322  
See also: Nature Biotechnology Review, Faculty of 1000 review
 
p53 binds preferentially to genomic region with high DNA-encoded nucleosome occupancy
Efrat Lidor Nili, Yair Field, Yaniv Lubling Jonathan Widom, Moshe Oren, Eran Segal  
Genome Research. 2010 Aug;17: doi-10.1101/gr.103945.109
 
Nucleosome sequence preferences influence in vivo nucleosome organization
Noam Kaplan, Irene Moore, Yvonne Fondufe-Mittendorf, Andrea J Gossett, Desiree Tillo, Yair Field, Timothy R Hughes, Jason D Lieb, Jonathan Widom & Eran Segal  
Nat Struct Mol Biol. 2010 Aug;17(8):918-20
 
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes
Miao-Chih Tsai, Ohad Manor, Yue Wan, Nima Mosammaparast, Jordon K. Wang, Fei Lan, Yang Shi, Eran Segal, Howard Y. Chang  
Science DOI: 10.1126/science.1192002, Published Online July 8, 2010
 
EGF Decreases the Abundance of MicroRNAs That Restrain Oncogenic Transcription Factors
Roi Avraham, Aldema Sas-Chen, Ohad Manor, Israel Steinfeld, Reut Shalgi, Gabi Tarcic, Noa Bossel, Amit Zeisel, Ido Amit, Yaara Zwang, Espen Enerly, Hege G. Russnes, Francesca Biagioni, Marcella Mottolese, Sabrina Strano, Giovanni Blandino, Anne-Lise Børresen-Dale, Yitzhak Pilpel, Zohar Yakhini, Eran Segal, and Yosef Yarden  
Sci. Signal., 1 June 2010 Vol. 3, Issue 124, p. ra43  
See also: Faculty of 1000 review
 
High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
Desiree Tillo, Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, Andrea J. Gossett, Yair Field, Jason D. Lieb, Jonathan Widom, Eran Segal, Timothy R. Hughes  
PLoS ONE 5(2): e9129. doi:10.1371/journal.pone.0009129
 
What controls nucleosome positions?
Eran Segal & Jonathan Widom  
Trends Genet. 2009 Jul 9. [Epub ahead of print]
 
From DNA sequence to transcriptional behaviour: a quantitative approach
Eran Segal & Jonathan Widom  
Nature Reviews Genetics, advance online publication, Published online 9 June 2009 (doi:10.1038/nrg2591)
 
Modeling interactions between adjacent nucleosomes improves genome-wide predictions of nucleosome occupancy
Shai Lubliner, Eran Segal  
Bioinformatics 2009 25: i348-i355.
 
Incorporating Nucleosomes into Thermodynamic Models of Transcription Regulation
Tali Raveh-Sadka, Michal Levo, Eran Segal  
Genome Res. 2009. 19:1480-1496
 
The DNA-encoded nucleosome organization of a eukaryotic genome
Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, Andrea J. Gossett, Desiree Tillo, Yair Field, Emily M. LeProust, Timothy R. Hughes, Jason D. Lieb, Jonathan Widom & Eran Segal  
Nature 458, 362-366 (19 March 2009)  
See also: Faculty of 1000 review
 
Poly(dA:dT) tracts: major determinants of nucleosome organization
Eran Segal and Jonathan Widom  
Curr Opin Struct Biol. 2009 Feb;19(1):65-71. Epub 2009 Feb 7
 
Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization
Yair Field, Yvonne Fondufe-Mittendorf, Irene K. Moore, Piotr Mieczkowski, Noam Kaplan, Yaniv Lubling, Jason D. Lieb, Jonathan Widom & Eran Segal  
Nature Genetics Published online: 1 March 2009 | doi:10.1038/ng.324  
See also: Highlight in Nature Reviews Genetics, Faculty of 1000 review.
 
Proteome-wide prediction of acetylation substrates
Amrita Basu, Kristie L. Rose, Junmei Zhang, Ronald C. Beavis, Beatrix Ueberheide, Benjamin A. Garcia, Brian Chait, Yingming Zhao, Donald F. Hunt, Eran Segal, C. David Allis and Sandra B. Hake  
Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13785-90. Epub 2009 Aug 3
 
Stemness, cancer, and cancer stem cells
David J. Wong, Eran Segal and Howard Y. Chang  
Cell Cycle. 2008 Dec 2;7(23). [Epub ahead of print]Click here to read
 
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Yair Field, Noam Kaplan, Yvonne Fondufe-Mittendorf, Irene K. Moore, Eilon Sharon, Yaniv Lubling, Jonathan Widom, Eran Segal  
PLoS Comput Biol 4(11): e1000216. doi:10.1371/journal.pcbi.1000216
 
Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation
Ophir Shalem, Orna Dahan, Michal Levo, Maria Rodriguez Martinez, Itay Furman, Eran Segal & Yitzhak Pilpel  
Molecular Systems Biology 4 Article number: 4 doi:10.1038/msb.2008.59, Published online: 14 October 2008  
See also: Faculty of 1000 review
 
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes
Michal Rabani, Michael Kertesz, Eran Segal  
Proc Natl Acad Sci U S A. 2008 Sep 24. [Epub ahead of print]
 
Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
Ji-Ping Wang, Yvonne Fondufe-Mittendorf, Liqun Xi, Guei-Feng Tsai, Eran Segal, Jonathan Widom  
PLoS Comput Biol 2008, September 12;4(9):e1000175
 
A Feature-Based Approach to Modeling Protein-DNA Interactions
Eilon Sharon, Shai Lubliner, Eran Segal.  
PLoS Comput Biol 2008, August 22;4(8):e1000154
 
Geometric constraints on neuronal connectivity facilitate a concise synaptic adhesive code
Shalev Itzkovitz, Leehod Baruch, Ehud Shapiro, and Eran Segal  
Proc Natl Acad Sci U S A. 2008 Jun 26. [Epub ahead of print]  
 
Estimating cell depth from somatic mutations
Adam Wasserstrom, Dan Frumkin, Rivka Adar, Shalev Itzkovitz, Tomer Stern, Shai Kaplan, Gabi Shefer, Irena Shur, Lior Zangi, Yitzhak Reizel, Alon Harmelin, Yuval Dor, Nava Dekel, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Shapiro  
PLoS Comput Biol. 2008 Apr 11;4(4):e1000058
 
Reconstruction of Cell Lineage Trees in Mice
Adam Wasserstrom, Rivka Adar, Gabi Shefer, Dan Frumkin, Shalev Itzkovitz, Tomer Stern, Irena Shur, Lior Zangi, Shai Kaplan, Alon Harmelin, Yair Reisner, Dafna Benayahu, Eldad Tzahor, Eran Segal, Ehud Shapiro  
PLoS ONE. 2008 Apr 9;3(4):e1939
 
Module map of stem cell genes guides creation of epithelial cancer stem cells
Wong DJ, Liu H, Ridky TW, Cassarino D, Segal E, Chang HY.  
Cell Stem Cell. 2008 Apr 10;2(4):333-44.  
See also: Faculty of 1000 review
 
Predicting expression patterns from regulatory sequence in Drosophila segmentation
Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall & Ulrike Gaul  
Nature 451, 535-540 (31 January 2008)  
See also: Editor Summary
 
Monoubiquitinated H2B is associated with the transcribed region of highly expressed genes in human cells
Neri Minsky, Efrat Shema, Yair Field, Meromit Schuster, Eran Segal & Moshe Oren  
Nature Cell Biology Published online: 16 March 2008, doi:10.1038/ncb1712
 
Systematic functional characterization of cis-regulatory motifs in human core promoters
Saurabh Sinha, Adam S. Adler, Yair Field, Howard Y. Chang, Eran Segal  
Genome Res. 18:477-488, 2008, Published online before print February 6, 2008, 10.1101/gr.6828808
 
Revealing Targeted Therapy for Human Cancer by Gene Module Maps
Wong DJ, Nuyten DS, Regev A, Lin M, Adler AS, Segal E, van de Vijver MJ, Chang HY.  
Cancer Res. 2008 Jan 15;68(2):369-78.
 
Reversal of aging by NFkappaB blockade
Adler AS, Kawahara TL, Segal E, Chang HY  
Cell Cycle. 2007 Dec 26;7(5) [Epub ahead of print]  
See also: Faculty of 1000 review  
 
Motif module map reveals enforcement of aging by continual NF-{kappa}B activity
Adler AS, Sinha S, Kawahara TL, Zhang JY, Segal E, Chang HY  
Genes Dev. 2007 Dec 15;21(24):3244-57. Epub 2007 Nov 30.  
See also: Genes & Development Cover, Faculty of 1000 review
 
The role of site accessibility in microRNA target recognition
Michael Kertesz, Nicola Iovino, Ulrich Unnerstall, Ulrike Gaul & Eran Segal  
Nature Genetics 39, 1278 - 1284 (2007).  
See also: News & Views, Research Highlights
 
InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
Haidong Wang, Eran Segal, Asa Ben-Hur, Qianru Li, Marc Vidal and Daphne Koller  
Genome Biology, 2007 8:R192 ( 14 September 2007 ).
 
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY.  
Cell 2007 Jun 29;129(7):1311-23.  
See also: News & Views, Faculty of 1000 review.
 
A Transcriptional Program Mediating Entry into Cellular Quiescence
Liu H, Adler AS, Segal E, Chang HY  
PLoS Genet. 2007 Jun 8;3(6):e91 [Epub ahead of print]
 
Decoding global gene expression programs in liver cancer by noninvasive imaging
Segal E, Sirlin CB, Ooi C, Adler AS, Gollub J, Chen X, Chan BK, Matcuk GR, Barry CT, Chang HY, Kuo MD  
Nature Biotechnology 25, 675 - 680 (2007)
 
Zinc-ion binding and cytokine activity regulation pathways predicts outcome in relapsing-remitting multiple sclerosis
Achiron A, Gurevich M, Snir Y, Segal E, Mandel M
Clin Exp Immunol. 2007 May 4  
 
A module of negative feedback regulators defines growth factor signaling
Amit I, Citri A, Shay T, Lu Y, Katz M, Zhang F, Tarcic G, Siwak D, Lahad J, Jacob-Hirsch J, Amariglio N, Vaisman N, Segal E, Rechavi G, Alon U, Mills GB, Domany E, Yarden Y  
Nature Genetics, 39, 503 - 512 (2007).
 
A Genomic Code for Nucleosome Positioning
E. Segal,Y. Fondufe-Mittendorf, L. Chen, A. Thastrom, Y. Field, I. K. Moore, J. Z. Wang, J. Widom.  
Nature, 2006 July, 442(7104):772-8  
See also: ESI Hot Paper, NY Times, Nature cover, News & Views, Nature Reviews Genetics, Faculty of 1000 review, Codes and Enigmas, TheScientist and about the authors.
 
Evidence for an instructive mechanism of de novo methylation in cancer cells.
I. Keshet., Y. Schlesinger, S. Farkash, E. Rand, M. Hecht, E. Segal, E. Pikarski, R.A. Young, A. Niveleau, H. Cedar, I. Simon.  
Nature Genetics, 2006 February, 38(2): 149-53.
 
Efficient Bundle Sorting
Y. Matias,E. Segal, J.S. Vitter  
SIAM Journal on Computing, 36(2):394-410, 2006.
 
From Signature to Models: Understanding Cancer Using Microarrays
E. Segal,N. Friedman, N. Kaminski, A. Regev, and D. Koller.  
Nature Genetics, 2005 June, 37(6 Suppl): S38-45.
 
A Module Map Showing Conditional Activity of Expression Modules in Cancer
E. Segal, N. Friedman, D. Koller, and A. Regev.  
Nature Genetics, 2004 October, 36(10): 1090-8.  
See also: Genome Biology highlight, Faculty of 1000 review.
 
Module Networks: Identifying Regulatory Modules and their Condition Specific Regulators from Gene Expression Data
E. Segal, M. Shapira, A. Regev, D. Pe'er, D. Botstein, D. Koller, and N. Friedman.  
Nature Genetics, 2003 June, 34(2): 166-76.
 
A Gene Co-Expression Network for Global Discovery of Conserved Genetics Modules
J. Stuart­*, E. Segal*, D. Koller, and S.Kim. (*equal contribution)  
Science, 2003 October, 302(5643): 249-55.  
See also: Science highlight, Faculty of 1000 review, Nature Reviews Genetics.
 
Learning Module Networks
E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman.  
Journal of Machine Learning Research (JMLR), 2005 April, 6(Apr): 557-88.  
An earlier version appeared in Proc. 19th Conference on Uncertainty in Artificial Intelligence (UAI)
 
A Discriminative Model for Identifying Spatial Cis-Regulatory Modules
E. Segal, R. Sharan.  
Journal of Computational Biology, 12(6): 822-34, August 2005.  
Recipient of the Best Paper by a Young Scientist Award at the 8th Inter. Conf. on Research in Computational Molecular Biology (RECOMB)
 
Probabilistic Discovery of Overlapping Cellular Processes and their Regulation Using Gene Expression Data
A. Battle, E. Segal, and D. Koller.  
Journal of Computational Biology, 12(7): 909-27, September 2005.  
An earlier version appeared at the 8th Inter. Conf. on Research in Computational Molecular Biology (RECOMB)
 
Genome-wide Discovery of Transcriptional Modules from DNA Sequence and Gene Expression
E. Segal, R. Yelensky, and D. Koller.  
Bioinformatics, 2003; 19(Suppl 1): 273-82.  
Recipient of the Best Paper Award at the 11th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB)
 
Discovering Molecular Pathways from Protein Interaction and Gene Expression Data
E. Segal, H. Wang, and D. Koller.  
Bioinformatics, 2003; 19(Suppl 1): 264-272.  
Recipient of the Best Student Paper Award at the 11th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB)
 
Rich Probabilistic Models for Gene Expression
E. Segal, B. Taskar, A. Gasch, N. Friedman, and D. Koller.  
Bioinformatics, 2003; 17 Suppl 1: S243-252.
 
Disruption of Yeast Forkhead-Associated Cell Cycle Transcription by Oxidative Stress
M. Shapira, E. Segal and D. Botstein.  
Molecular Biology of the Cell, 34(2): 166-76, October 2004.
 
A Transcriptional Profile of Aging in the Human Kidney
G.J. Rodwell, R. Sonu, J.M. Zahn, J.Lund, J. Wilhelmy, L. Wang, W. Xiao, M. Mindrinos, E. Crane, E. Segal, B.D. Myers, J.D. Brooks, R.W. Davis, J. Higgins, A.B. Owen, S.K. Kim.  
PLoS Biology, 2(12): e427, November 2004.
 
Sfp1 is a Stress- and Nutrient-Sensitive Regulator of Ribosomal Protein Gene Expression
R.M. Marion, A. Regev, E. Segal, Y. Barash, N. Friedman, D. Koller, and E. O'Shea.  
PNAS, 2004 October, 101(40):14315-22.
 

Conference Publications


< 2010 Dec 22.tr> 2010 Dec 22.
A Feature-Based Approach to Modeling Protein-DNA Interactions
E. Sharon and E. Segal  
In 11th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), 2007
 
Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale
H. Wang, E. Segal, A. Ben-Hur, D. Brutlag, and D. Koller.  
In Proc. 18th Inter. Conf. on Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, 2004
 
GeneXPress: A Visualization and Statistical Analysis Tool for Gene Expression and Sequence Data
E. Segal, R. Yelensky, A. Kaushal, T. Pham, A. Regev, D. Koller, and N. Friedman.  
Proceedings of the 11th Inter. Conf. on Intelligent Systems for Molecular Biology (ISMB), 2004
 
Decomposing Gene Expression into Cellular Processes
E. Segal, A. Battle, D. Koller.  
In Proc. 8th Pacific Symposium on Biocomputing (PSB), Kaua'i, January 2003
 
Boosting Density Estimation
S. Rosset,E. Segal.  
In Proc. 16th Inter. Conf. on Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, 2002
 
From Promoter Sequence to Expression: A Probabilistic Framework
E. Segal, Y. Barash, I. Simon, N. Friedman, and D. Koller.  
In Proc. 6th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), Washington, DC, April 2002.
 
Probabilistic Hierarchical Clustering for Biological Data
E. Segal, D.Koller.  
In Proc. 6th Inter. Conf. on Research in Computational Molecular Biology (RECOMB), Washington, DC, April 2002
 
Probabilistic Abstraction Hierarchies
E. Segal, D. Koller, D. Ormoneit.  
In Proc. 15th International Conference on Neural Information Processing Systems (NIPS), Vancouver, British Columbia, Canada, 2001
 
Probabilistic Classification and Clustering in Relational Data
B. Taskar, E. Segal, and D. Koller  
In Proc. 17th Inter. Joint Conference on Artificial Intelligence (IJCAI), Seattle, Washington, August 2001
 
Exact Inference in Networks with Discrete Children of Continuous Parents
U. Lerner, E. Segal and D. Koller  
In Proc. 17th Conf. on Uncertainty in Artificial Intelligence (UAI), Seattle, Washington, August 2001
 
Probabilistic Models of Text and Link Structure for Hypertext Classification
L. Getoor,E. Segal, B. Taskar and D. Koller  
In IJCAI Workshop on "Text Learning: Beyond Supervision", Seattle, Washington, August 2001
 
Efficient Bundle Sorting
Y. Matias,E. Segal, J.S. Vitter  
In Proc. 11th Annual SIAM/ACM Symposium on Discrete Algorithms (SODA), San-Francisco, California, January 2000